X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=1fbb82ee5f6af3ccd1bacdb8c3086e5593adae3f;hb=97acc4fa0742948992abd1f3ca982c6df4eff653;hp=f1464b62e426cb2e6ecd6cd7944596af125bdbcc;hpb=16c8c9d35fd5aa1c33afbcf778564e766e72e02a;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index f1464b6..1fbb82e 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -28,6 +28,7 @@ import java.applet.*;
 
 import java.awt.*;
 import java.awt.event.*;
+import jalview.appletgui.FeatureSettings;
 
 
 /**
@@ -46,7 +47,7 @@ public class JalviewLite extends Applet
 
     //The currentAlignFrame is static, it will change
     //if and when the user selects a new window
-    static AlignFrame currentAlignFrame;
+    public static AlignFrame currentAlignFrame;
 
     //This is the first frame to be displayed, and does not change
     AlignFrame initialAlignFrame;
@@ -177,6 +178,8 @@ public class JalviewLite extends Applet
             {
                 public void windowClosing(WindowEvent e)
                 {
+                  if(frame instanceof AlignFrame)
+                    ((AlignFrame)frame).closeMenuItem_actionPerformed();
                     if(currentAlignFrame == frame)
                     {
                       currentAlignFrame = null;
@@ -277,6 +280,7 @@ public class JalviewLite extends Applet
             file = _file;
             if(file.startsWith("PASTE"))
             {
+              file = file.substring(5);
               protocol = AppletFormatAdapter.PASTE;
             }
             else if(inArchive(file))
@@ -307,6 +311,8 @@ public class JalviewLite extends Applet
                                                  file,
                                                  embedded);
 
+              if(protocol==jalview.io.AppletFormatAdapter.PASTE)
+                currentAlignFrame.setTitle("Sequences from "+getDocumentBase());
 
               initialAlignFrame = currentAlignFrame;
 
@@ -315,7 +321,8 @@ public class JalviewLite extends Applet
 
                 String treeFile = applet.getParameter("tree");
                 if(treeFile==null)
-                  applet.getParameter("treeFile");
+                  treeFile = applet.getParameter("treeFile");
+
                 if (treeFile != null)
                 {
                   try
@@ -356,7 +363,7 @@ public class JalviewLite extends Applet
               if(param !=null && param.equalsIgnoreCase("true"))
               {
                 currentAlignFrame.viewport.showSequenceFeatures(true);
-                currentAlignFrame.featureSettings_actionPerformed();
+                new FeatureSettings(currentAlignFrame.alignPanel);
               }
 
              param = getParameter("annotations");